Trackers in re-linked footage don't match the features on video
The trackers on the linked footage do not match with any trackable features in the video.



it looks like you are using some frame offset (the 1st frame in the composition and the 1st frame of the video file are not the same) 
Somehow the offset information got lost in the re-link or at some point it changed in the file (my guessing powers are quite limited).
You might need to find the correct start frame manually by sliding the Offset (place the cursor over the Offset box, right click with the mouse and drag to visually find the point where your trackers and the image match correctly)
If you offset the image by 500 frames things line up better.